The response speed is awesome! On github Eric answered: https://github.com/galaxyproject/tools-iuc/blob/0887009a23d176b21536c9fd8a18...
see L12 of that file for where the bai file is stored.
That explains a lot. Very precise example. Thank you! What I'm still wondering is: When is it being generated, what code is used for that? More specific: When I use Picard SortSam in galaxy, the output is a bam file with an accompanying bai file. But when I use Picard on command line, the output is just a bam file. In the Picard SortSam galaxy tool, it is not being done. (If I didn't miss something) What leads me to When I do multiple actions with my bam file - is the index generated every
time? (overhead)
GATK processes BAM files and at the same time the bai files. It would be a waste to just use the bam files and re-generate the bai files, that already exist. How could that be done? Thanks, Alexander 2015-06-18 18:44 GMT-05:00 Alexander Vowinkel <vowinkel.alexander@gmail.com> :
Hi,
when I 'produce' a bam file in my output, I can download the bam file and a corresponding bai file.
I am now wondering where does the bai file come from? When is it being generated, what code is used for that? When I do multiple actions with my bam file - is the index generated every time? (overhead) Where is the bai saved on disk (if it is)?
I found that in the IUC gatk, a new bai is always generated when a gatk tool is started. This creates quite an overhead. Isn't there a better solution?
@ref https://github.com/galaxyproject/tools-iuc/issues/194
Best, Alexander